In January 2015, police commandos killed Zulkifli Abdhir, who was on the United States government's list of "most wanted terrorists", in a raid on a remote farmland area in the south, where various Muslim separatist rebel groups and other fighters are based.

Gunmen ambushed the attacking police commandos and killed 44 of them in a day-long battle. A Philippine Senate investigation blamed poor planning and coordination for the deaths.

The raid was carried out during the term of Duterte's predecessor Aquino, derailing efforts to make a peace pact with the main Muslim separatist group, the Moro Islamic Liberation Front (MILF).

Duterte's statement on Tuesday was the first time a Filipino official publicly linked the CIA to the incident.

During his seven months in office, Duterte has sought to loosen the Philippines' longtime alliance with the US, while forging closer ties with China and Russia.

'US forces on the scene'

Aquino had justified the police raid, saying that Zulkifli had been training armed fighters in the southern Philippines to make bombs.

The US had said Zulkifli was a top fighter of the Southeast Asian armed group Jemaah Islamiyah.

A Philippine Senate report into the raid later concluded the US played a "substantial" role by providing training, equipment and intelligence to the Filipino forces.

The Senate report did not refer to the CIA.

In a statement to Al Jazeera, Molly Koscina, spokesman of the US Embassy in Manila said, "We renew our heartfelt condolences to the family members of those who died trying to bring peace and stability to Mindanao.

"This operation was planned and executed by Philippine authorities. We refer you to them for details of the operation."

Jose Torres, a Filipino journalist who frequently covers the Mindanao conflict, told Al Jazeera that any CIA involvement remained unclear.

"What is clear, however, was US forces were on the scene of the incident. The US did not deny it. Some US military men were confirmed to be with their Filipino counterparts a few kilometres away," Torres said.

Torres also said unnamed sources privy to the operation said some "Caucasian-looking men" were among the casualties.